Job ID = 6454780 SRX = SRX2592383 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:52:56 prefetch.2.10.7: 1) Downloading 'SRR5289660'... 2020-06-21T09:52:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:56:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:56:13 prefetch.2.10.7: 1) 'SRR5289660' was downloaded successfully Read 17614420 spots for SRR5289660/SRR5289660.sra Written 17614420 spots for SRR5289660/SRR5289660.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:00 17614420 reads; of these: 17614420 (100.00%) were unpaired; of these: 1593932 (9.05%) aligned 0 times 13253870 (75.24%) aligned exactly 1 time 2766618 (15.71%) aligned >1 times 90.95% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7782821 / 16020488 = 0.4858 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:08:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:08:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:21: 1000000 INFO @ Sun, 21 Jun 2020 19:08:29: 2000000 INFO @ Sun, 21 Jun 2020 19:08:37: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:08:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:45: 4000000 INFO @ Sun, 21 Jun 2020 19:08:51: 1000000 INFO @ Sun, 21 Jun 2020 19:08:53: 5000000 INFO @ Sun, 21 Jun 2020 19:08:59: 2000000 INFO @ Sun, 21 Jun 2020 19:09:02: 6000000 INFO @ Sun, 21 Jun 2020 19:09:08: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:09:11: 7000000 INFO @ Sun, 21 Jun 2020 19:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:09:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:17: 4000000 INFO @ Sun, 21 Jun 2020 19:09:19: 8000000 INFO @ Sun, 21 Jun 2020 19:09:21: 1000000 INFO @ Sun, 21 Jun 2020 19:09:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:22: #1 total tags in treatment: 8237667 INFO @ Sun, 21 Jun 2020 19:09:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:09:22: #1 tags after filtering in treatment: 8237483 INFO @ Sun, 21 Jun 2020 19:09:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:23: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 19:09:23: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:24: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:09:24: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.05_model.r INFO @ Sun, 21 Jun 2020 19:09:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:26: 5000000 INFO @ Sun, 21 Jun 2020 19:09:30: 2000000 INFO @ Sun, 21 Jun 2020 19:09:35: 6000000 INFO @ Sun, 21 Jun 2020 19:09:39: 3000000 INFO @ Sun, 21 Jun 2020 19:09:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:44: 7000000 INFO @ Sun, 21 Jun 2020 19:09:48: 4000000 INFO @ Sun, 21 Jun 2020 19:09:53: 8000000 INFO @ Sun, 21 Jun 2020 19:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:55: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (271 chroms): 3 millis pass2 - checking and writing primary data (13015 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:56: #1 total tags in treatment: 8237667 INFO @ Sun, 21 Jun 2020 19:09:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:09:56: #1 tags after filtering in treatment: 8237483 INFO @ Sun, 21 Jun 2020 19:09:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:57: 5000000 INFO @ Sun, 21 Jun 2020 19:09:58: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 19:09:58: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:58: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:09:58: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.10_model.r INFO @ Sun, 21 Jun 2020 19:09:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:06: 6000000 INFO @ Sun, 21 Jun 2020 19:10:15: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:25: 8000000 INFO @ Sun, 21 Jun 2020 19:10:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:27: #1 total tags in treatment: 8237667 INFO @ Sun, 21 Jun 2020 19:10:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:10:28: #1 tags after filtering in treatment: 8237483 INFO @ Sun, 21 Jun 2020 19:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:29: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 19:10:29: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:29: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:10:29: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.20_model.r INFO @ Sun, 21 Jun 2020 19:10:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:30: Done! pass1 - making usageList (209 chroms): 3 millis pass2 - checking and writing primary data (10917 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:10:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592383/SRX2592383.20_summits.bed INFO @ Sun, 21 Jun 2020 19:11:01: Done! pass1 - making usageList (125 chroms): 3 millis pass2 - checking and writing primary data (8493 records, 4 fields): 18 millis CompletedMACS2peakCalling